Data Publication for UC Davis Publish or Perish
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Transcript of Data Publication for UC Davis Publish or Perish
Publish or Perish, UC Davis February 2014
Data Publication Etcetera at the CDL
Carly Strasser & John Kratz California Digital Library
@carlystrasser
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Back in the day…
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Back in the day…
Da Vinci
Curie Newton
classicalschool.blogspot.com
Darwin
Research has changed
Better Worse
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Such Internet!
So many tools!
From Flickr by John Jobby
So much data!
Research has changed Worse
Digital data Fr
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Ideas, data, analysis
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Most marine benthic invertebrate life cycles include a plank-tonic larval phase that facilitates dispersal among adult popula-tions (Thorson 1950). Connectivity, or the degree to which geo-graphically separated populations exchange individuals, is animportant factor in the spatial population dynamics of manymarine organisms (Moilanen and Nieminen 2002). An under-standing of connectivity in marine benthic populations isimportant because of the role spatial dynamics play in fisheriesmanagement and the design and implementation of marineprotected areas. However, studying larval dispersal is challeng-ing due to small larval sizes, high dilution rates, and high larvalmortality rates (Thorson 1950, 1966).
In recent years, the use of artificial and natural tags to trackmarine larvae has been explored (e.g., Levin 1990; Thorrold etal. 2002). One type of natural tag that may be useful for identi-fying natal origins is elemental signatures recorded in biogenic
carbonate. This technique relies on the observation that someelements are incorporated into the calcium carbonate matrixin amounts that are related to the dissolved concentrationsand physical properties of the ambient water (e.g., Bath et al.2000; Elsdon and Gillanders 2003; Fowler et al. 1995; Thorroldet al. 1997; Vander Putten et al. 2000). Provided water chem-istry or temperature is significantly different among natalhabitats, such variation can serve as a natural tag, or signature,of the geographic origin of organisms. The use of geochemicalsignatures in fish otoliths as natural tags for population stud-ies is well established (Campana and Thorrold 2001). Recentefforts have expanded the use of elemental tags to inverte-brates including decapods (DiBacco and Levin 2000), gas-tropods (Zacherl et al. 2003), bivalves (Becker et al. 2005), andcephalopods (Arkhipkin et al. 2004).
Most studies attempting to obtain time-resolved elementalsignatures from calcified tissues have used laser ablation induc-tively coupled plasma mass spectrometry (ICP-MS). Conven-tional solution-based ICP-MS analyses are generally more pre-cise than laser ablation assays but lack the ability to resolveelemental signatures from individual life stages (Campana et al.1997). Laser ablation ICP-MS is particularly useful for larvalstudies because it allows the core of an otolith or the larval shellof a juvenile bivalve to be targeted. Yet, surprisingly few studieshave empirically tested the effective spatial resolution of laser
Laser ablation ICP-MS analysis of larval shell in softshell clams(Mya arenaria) poses challenges for natural tag studiesC.A. Strasser, S.R. Thorrold, V.R. Starczak, and L.S. MullineauxWoods Hole Oceanographic Institution, Woods Hole, MA 02543
AbstractWe investigated whether laser ablation inductively coupled plasma mass spectrometry (ICP-MS) could be used
to quantify larval shell compositions of softshell clams, Mya arenaria. The composition of aragonitic otoliths hasbeen used as a natural tag to identify natal habitat in connectivity studies of fish. If it is possible to measure lar-val shell reliably, this technique could also be applied to marine bivalves. To determine whether the first larvalshell (prodissoconch I) could be measured independent of underlying material, we conducted laboratory exper-iments in which larval M. arenaria were exposed to enrichments of the stable isotope 138Ba during different stagesin shell development. We were unable to isolate the chemical signature of the prodissoconch I from subsequentlife stages in all combinations of shell preparation and instrument settings. Typical instrument settings burnedthrough the prodissoconch I on a post-settlement juvenile and at least 9 d of second larval shell (prodissoconch II)growth. Our results suggest instrumental and technical improvements are needed before laser ablation ICP-MScan be useful for connectivity studies that require analysis of larval shell on a post-settlement M. arenaria juve-nile. Laser burn-through is potentially a problem in any connectivity study where it is necessary to assay thesmall amounts of shell material that are deposited before a larva disperses away from its natal location.
AcknowledgmentsThis work was supported by NSF project numbers OCE-0241855 andOCE-0215905. Special thanks to Henry Lind of the Eastham Departmentof Natural Resources for supplying clams and culturing expertise, and toDiane Adams, Benjamin Walther, Travis Elsdon, Anne Cohen, Dale Leavitt,Phil Alatalo, and Susan Mills for helpful discussions. We also thank D.Zacherl and an anonymous reviewer for their helpful comments.
Limnol. Oceanogr.: Methods 5, 2007, 241–249© 2007, by the American Society of Limnology and Oceanography, Inc.
LIMNOLOGYand
OCEANOGRAPHY: METHODS
Provenance
“Reproducibility Crisis”
“Digital Dark Age”
“Erosion of Trust”
Can we fix science? the way we
communicate our
v Change nothing
Change everything
Change nothing
Change everything
work within publishing paradigm
take advantage of new tools
incentivize sharing, reproducibility
From Flickr by Leo Reynolds
We are in the midst of a culture shift.
What will scholarly communication look like in 10 years?
notebook science source content access data government repository knowledge Fr
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by
cdse
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Enable data sharing Encourage
new incentives
Think about code sharing
Work with libraries, publishers and
researchers
Explore new tools to help
change system
Build tools
Create and manage persistent identifiers ARKs, DOIs, etc.
Platform for publishing + repository for OA publications
“Data Publication”
John Kratz, CLIR Postdoc
What does “data publication” mean? 1. Available 2. Citable 3. Trustworthy*
Data are
*peer reviewed? certified?
Available | Citable | Trustworthy
Publish means to “make public”. You should not have to email the author. The data doesn’t have to be open access. Where to publish?
“Email me!” CC-0 on web
Repository choices…
Repositories for data
General content
Non-institutional
Institutional
Discipline-specific
Repository choices…
Simple case…
Data citations should be in reference list. Five-element citation: author, year, title, publisher, identifier
Available | Citable | Trustworthy
Boettiger C, Dushoff J, Weitz JS (2009). Data from: Fluctuation domains in adaptive evolution. Theoretical Population Biology. Published in Dryad. doi:10.5061/dryad.j8n0p7vc
More complicated…
Deep data citation: what if you want to cite a subset? Dynamic data: how to create a reliable citation when a dataset is changing?
Available | Citable | Trustworthy
Technical VS. Scientific
Package review: data + paper
Sometimes consider impact and/or novelty
Guidelines provided
Available | Citable | Trustworthy
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1. Traditional article: Data published
alongside a traditional journal article.
Example: Supplemental material hosted by the journal publisher. Available + citable. Review is up to the journal
What does a data publication look like?
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2. Data paper: Data published alongside a
descriptive “data paper”.
Most require data be in a trusted repository. All have a component of peer review. What they are NOT: results, analysis, conclusions. Examples: • Standalone journals: Nature Scientific Data, Geoscience Data
Journal, Ecological Archives • Journals that publish data papers: GigaScience, F1000 Research,
Internet Archaeology
What does a data publication look like?
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3. Standalone data: Data published without a
related journal article.
Rich metadata (structured or unstructured) Examples: • Open Context • NASA PDS Peer Review Data • figshare (but no validation)
What does a data publication look like?
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Change nothing
Change everything
?
Beyond Data… Code! Workflows!
…?
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From Flickr by dotpolka
Scholarly communication is changing – for the better.
Website Email Tweet Slides
carlystrasser.net [email protected] @carlystrasser slideshare.net/carlystrasser
Big thanks to John Kratz, CLIR Postdoc